plotMultiNMR: A function for plotting NMR spectra.

In mrbin: Metabolomics Data Analysis Functions

A function for plotting NMR spectra.

Description

This function plots the current NMR spectrum. If no parameters are provided, parameters are read from the mrbin.env environment variables, set by mrbin. To change the plot, use zoom(), zoomIn(), zoomOut(), intPlus(), intMin(), left(), right(). For 2D data use additionally: contMin(), contPlus(), up(), down()

Usage

plotMultiNMR(
  region = NULL,
  rectangleRegions = NULL,
  rectangleColors = c("darkseagreen3", "orange", "blue", "red", "yellow", "gray",
    "purple"),
  density = NULL,
  cex.axis = 0.7,
  rectangleFront = FALSE,
  correctOffset2D = TRUE,
  polygonRegion = NULL,
  maxPlots = Inf,
  setContours = TRUE,
  color = NULL,
  add = FALSE,
  showGrid = FALSE,
  buffer = TRUE,
  manualScale = TRUE,
  plotTitle = "",
  renewSpectrum = TRUE,
  restrictToRange = FALSE,
  enableSplit = TRUE,
  dimension = NULL,
  lwd = 1,
  background = NULL,
  titles = NULL,
  plotCurrent = TRUE,
  ...
)

Arguments

region	A vector defining the plot region (left, right, top, bottom) or "all" for the whole spectrum
rectangleRegions	A 4-column matrix defining areas where to plot rectangles
rectangleColors	Define colors for the rectangles
density	Shading lines for the rectangles
cex.axis	Font size of axis tick labels.
rectangleFront	Plot rectangles in front of spectrum rather than in background (only 2D)
correctOffset2D	Do a basic offset correction so 2D spectra have a baseline close to 0. Defaults to TRUE
polygonRegion	Defines 4 corners of a polygon to be plotted
maxPlots	The maximum number of 2D plots to be overlaid
setContours	Should upper and lower contour levels be calculated of the old ones be reused? Default: TRUE
color	Defines the color of the spectrum plot. If NULL, a rainbow theme is used for 2D NMR
add	If TRUE, additional spectrum plots are overlaid with the current plot
showGrid	Shows a grid of data points. Defaults to FALSE
buffer	Speed up plotting by loading a plot. Defaults to TRUE
manualScale	If TRUE, scaling factor is taken from environment variables
plotTitle	Defines the main title of the plot
renewSpectrum	Should a new size-reduced spectrum for quicker plotting be calculated, or can the old one be used? Default: TRUE
restrictToRange	Restrict plot area to range of available data points. Defaults to FALSE
enableSplit	Allow split plots for showing 1D and 2D spectra simultaneously
dimension	If not provided, this will be taken from package environment
lwd	Line width, defaults to 1
background	Background color, defaults to NULL (no background fill, usually results in a white background)
titles	Display list of spectrum titles in plot, defaults to NULL
plotCurrent	Should the first (current) spectrum in the list be plotted, defaults to TRUE
...	Additional graphical parameters that will be passed to the functions plot, lines, and/or contour

Value

None

Examples

mrbin(silent=TRUE,setDefault=TRUE,parameters=list(dimension="1D",binwidth1D=.1,
         PQNScaling="No",noiseRemoval="No",trimZeros="No",tryParallel=TRUE,
         fixNegatives="No",logTrafo="No",PCA="No",verbose=TRUE,
         NMRfolders=system.file("extdata/1/10/pdata/10",package="mrbin")))
plotMultiNMR()

mrbin documentation built on April 4, 2025, 5:24 a.m.